Nitrite-dependent anaerobic methane oxidation (n-damo) is a novel pathway for controlling methane emissions from paddy ecosystems. However, the contribution of n-damo to methane oxidation and its response to elevated atmospheric CO2 concentration are poorly known. Here, an ambient CO2 treatment (CK) and a slow increase of atmospheric CO2 treatment (EC: an increase of 40 μL·L-1 per year above CK until 160 μL·L-1) were set up based on the CO2 automatic control platform with open top chambers. The stable isotope tracer experiment, quantitative PCR and high-throughput sequencing were employed to investigate the n-damo activity, abundance, diversity and community composition of Candidatus Methylomirabilis oxyfera (M. oxyfera)-like bacteria in paddy soils across key rice growth stages (tillering, jointing and flowering stages) under different CO2 treatments. The results showed that EC treatment stimulated the n-damo activity and abundance of M. oxyfera-like bacteria, particularly at the jointing stage. Further, EC treatment significantly changed the community composition and diversity of M. oxyfera-like bacteria. The variations in soil dissolved organic carbon content and inorganic nitrogen content under EC treatment could probably cause the change of n-damo activity and the community structure of M. oxyfera-like bacteria. Taken together, our results showed a positive response of n-damo to the slow increase of atmospheric CO2 concentration, suggesting its active role in reducing methane emissions from paddy fields under the future climate conditions.